Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397263.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_86.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8461613
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 85630 characters in sequence are not A, C, G, or T
File 2 of 18
Found at i:756727 original size:7 final size:7
Alignment explanation
Indices: 756715--756749 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
756705 ATATAGCATC
756715 ATTGCCA
1 ATTGCCA
756722 ATTGCCA
1 ATTGCCA
756729 ATTGCCA
1 ATTGCCA
*
756736 ACTGCCA
1 ATTGCCA
756743 ATTGCCA
1 ATTGCCA
756750 TCTCTCTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (7 bp):
ATTGCCA
Found at i:765310 original size:63 final size:63
Alignment explanation
Indices: 765230--765354 Score: 223
Period size: 63 Copynumber: 2.0 Consensus size: 63
765220 TTTTGATACA
*
765230 GCTTATGCAGCTATATTTTTTGTTCTGCCATGATTTTGAGTAGTCTTTGTTTGCATTTTTTTT
1 GCTTATGCAGCTATATTTTTTGTTCTGCCATGATATTGAGTAGTCTTTGTTTGCATTTTTTTT
* *
765293 GCTTATGCAGCTGTATTTTTTGTTCTGCCATGATATTGAGTAGTCTTTGTTTGTATTTTTTT
1 GCTTATGCAGCTATATTTTTTGTTCTGCCATGATATTGAGTAGTCTTTGTTTGCATTTTTTT
765355 CTTTATCATT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.14, C:0.12, G:0.18, T:0.55
Consensus pattern (63 bp):
GCTTATGCAGCTATATTTTTTGTTCTGCCATGATATTGAGTAGTCTTTGTTTGCATTTTTTTT
Found at i:767970 original size:37 final size:37
Alignment explanation
Indices: 767900--767971 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
767890 CTCAACTTAG
* **
767900 TACATAAGTTTGTGAGATATAATTATATTGCTTATCA
1 TACATAAGCTTGTGAGATATAATTATACAGCTTATCA
767937 TACATAAGCTTGTGAGATATAATTATACAGCTTAT
1 TACATAAGCTTGTGAGATATAATTATACAGCTTAT
767972 TACAACAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (37 bp):
TACATAAGCTTGTGAGATATAATTATACAGCTTATCA
Found at i:784985 original size:42 final size:42
Alignment explanation
Indices: 784935--785061 Score: 254
Period size: 42 Copynumber: 3.0 Consensus size: 42
784925 ACTTATCCGT
784935 TATTCTGTTCCTTGCTCCTCAATTACAGTTGAACACTTTTTC
1 TATTCTGTTCCTTGCTCCTCAATTACAGTTGAACACTTTTTC
784977 TATTCTGTTCCTTGCTCCTCAATTACAGTTGAACACTTTTTC
1 TATTCTGTTCCTTGCTCCTCAATTACAGTTGAACACTTTTTC
785019 TATTCTGTTCCTTGCTCCTCAATTACAGTTGAACACTTTTTC
1 TATTCTGTTCCTTGCTCCTCAATTACAGTTGAACACTTTTTC
785061 T
1 T
785062 CTTAACGCTG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 85 1.00
ACGTcount: A:0.19, C:0.26, G:0.09, T:0.46
Consensus pattern (42 bp):
TATTCTGTTCCTTGCTCCTCAATTACAGTTGAACACTTTTTC
Found at i:804794 original size:64 final size:62
Alignment explanation
Indices: 804642--804803 Score: 168
Period size: 64 Copynumber: 2.6 Consensus size: 62
804632 TCTTTTCGCG
* * * *
804642 ATACATTTATATA-TAAAATCAAGA-TTTCATTAATATAATTAATTCTACGTGTTCACACAC
1 ATACATTTATATATTAAATTCAAGATTTTAATTAATATAATTAATTCTACATATTCACACAC
* * * * * *
804702 ATACAATTATATATTAAATTTAAAATTTTAATTAATTTGATTAATTTTACATATTCACACGTAC
1 ATACATTTATATATTAAATTCAAGATTTTAATTAATATAATTAATTCTACATATTCACAC--AC
* *
804766 ATACATTTATACATTAAATTCGAGATTTT-ATTGAATAT
1 ATACATTTATATATTAAATTCAAGATTTTAATT-AATAT
804804 GATCATTTGA
Statistics
Matches: 81, Mismatches: 16, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
60 12 0.15
61 8 0.10
62 28 0.35
63 3 0.04
64 30 0.37
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (62 bp):
ATACATTTATATATTAAATTCAAGATTTTAATTAATATAATTAATTCTACATATTCACACAC
Found at i:807526 original size:19 final size:18
Alignment explanation
Indices: 807489--807527 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
807479 TGATTATATT
*
807489 ATATAATATAAAGACTAC
1 ATATAATATAAAAACTAC
*
807507 ATATAATAATAAAAATTAC
1 ATATAAT-ATAAAAACTAC
807526 AT
1 AT
807528 TTTAATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (18 bp):
ATATAATATAAAAACTAC
Found at i:807595 original size:46 final size:46
Alignment explanation
Indices: 807540--807674 Score: 270
Period size: 46 Copynumber: 2.9 Consensus size: 46
807530 TAATATTATT
807540 ATTAAAATGCAAATTTATTTACTAATTCAAGATAATTTTAACAATC
1 ATTAAAATGCAAATTTATTTACTAATTCAAGATAATTTTAACAATC
807586 ATTAAAATGCAAATTTATTTACTAATTCAAGATAATTTTAACAATC
1 ATTAAAATGCAAATTTATTTACTAATTCAAGATAATTTTAACAATC
807632 ATTAAAATGCAAATTTATTTACTAATTCAAGATAATTTTAACA
1 ATTAAAATGCAAATTTATTTACTAATTCAAGATAATTTTAACA
807675 TTCAATTGTT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 89 1.00
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.39
Consensus pattern (46 bp):
ATTAAAATGCAAATTTATTTACTAATTCAAGATAATTTTAACAATC
Found at i:815405 original size:12 final size:12
Alignment explanation
Indices: 815381--815418 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
815371 CAAGAAACAA
815381 ACTCCACCC-CCC
1 ACTCC-CCCTCCC
815393 ACTCCCCCTCCC
1 ACTCCCCCTCCC
*
815405 ACTCCCACTCCC
1 ACTCCCCCTCCC
815417 AC
1 AC
815419 CCATTGTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 3 0.12
12 21 0.88
ACGTcount: A:0.16, C:0.71, G:0.00, T:0.13
Consensus pattern (12 bp):
ACTCCCCCTCCC
Found at i:819409 original size:22 final size:22
Alignment explanation
Indices: 819384--819434 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
819374 AAATGGACTC
*
819384 TTGTTTTATTAAGTCAATGCTG
1 TTGTTCTATTAAGTCAATGCTG
819406 TTGTTCTATTAAGTCAATGCTG
1 TTGTTCTATTAAGTCAATGCTG
819428 TTGTTCT
1 TTGTTCT
819435 TAGTTCGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.12, G:0.18, T:0.51
Consensus pattern (22 bp):
TTGTTCTATTAAGTCAATGCTG
Found at i:826517 original size:19 final size:19
Alignment explanation
Indices: 826493--826531 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
826483 AATGTTTGTG
826493 ACAAAATAAATATGACCAA
1 ACAAAATAAATATGACCAA
826512 ACAAAATAAATATGACCAA
1 ACAAAATAAATATGACCAA
826531 A
1 A
826532 TATAAAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.64, C:0.15, G:0.05, T:0.15
Consensus pattern (19 bp):
ACAAAATAAATATGACCAA
Found at i:833679 original size:21 final size:21
Alignment explanation
Indices: 833634--833698 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
833624 CCAAGAAGCT
* *
833634 CTTGGTTCATCAAAGGAATAT-
1 CTTGGATCATCAAACG-ATATC
833655 CTTGGATCATCAAACGATATC
1 CTTGGATCATCAAACGATATC
* *
833676 CTT-GCTGCATCAAACGACATC
1 CTTGGAT-CATCAAACGATATC
833697 CT
1 CT
833699 CCCAGCATCA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.16
21 32 0.84
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (21 bp):
CTTGGATCATCAAACGATATC
Found at i:833706 original size:21 final size:21
Alignment explanation
Indices: 833662--833709 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
833652 TATCTTGGAT
* ** *
833662 CATCAAACGATATCCTTGCTG
1 CATCAAACGACATCCTCCCAG
833683 CATCAAACGACATCCTCCCAG
1 CATCAAACGACATCCTCCCAG
833704 CATCAA
1 CATCAA
833710 GTGAAAACCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.35, G:0.10, T:0.21
Consensus pattern (21 bp):
CATCAAACGACATCCTCCCAG
Found at i:835164 original size:25 final size:25
Alignment explanation
Indices: 835136--835183 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
835126 CATACTAAGG
835136 GGAAAAAAAAAGTAAAAAAAGGTTA
1 GGAAAAAAAAAGTAAAAAAAGGTTA
* * * *
835161 GGAAAGAAAGATTAAAGAAAGGT
1 GGAAAAAAAAAGTAAAAAAAGGT
835184 GAAACCATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.25, T:0.12
Consensus pattern (25 bp):
GGAAAAAAAAAGTAAAAAAAGGTTA
Found at i:852111 original size:4 final size:4
Alignment explanation
Indices: 852089--852127 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
852079 TAACCTCCTT
* * *
852089 TATA CATA TACA TACA TATA TATA TATA TATA TATA TAT
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TAT
852128 CTCCAAAGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (4 bp):
TATA
Found at i:852119 original size:10 final size:10
Alignment explanation
Indices: 852089--852127 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
852079 TAACCTCCTT
852089 TATACATATA
1 TATACATATA
*
852099 CATACATATA
1 TATACATATA
*
852109 TATATATATA
1 TATACATATA
*
852119 TATATATAT
1 TATACATAT
852128 CTCCAAAGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (10 bp):
TATACATATA
Found at i:852127 original size:6 final size:6
Alignment explanation
Indices: 852089--852127 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
852079 TAACCTCCTT
* * *
852089 TATACA TATACA TACATA TATATA TATATA TATATA TAT
1 TATATA TATATA TATATA TATATA TATATA TATATA TAT
852128 CTCCAAAGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (6 bp):
TATATA
Found at i:856045 original size:18 final size:18
Alignment explanation
Indices: 856024--856059 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
856014 TAAAAATTAA
856024 AAAAATTGAAAAGAGAAG
1 AAAAATTGAAAAGAGAAG
* *
856042 AAAAATTTAAAGGAGAAG
1 AAAAATTGAAAAGAGAAG
856060 GGCAAATCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.22, T:0.14
Consensus pattern (18 bp):
AAAAATTGAAAAGAGAAG
Found at i:856550 original size:3 final size:3
Alignment explanation
Indices: 856544--856570 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
856534 TGCTTCATTA
856544 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
856571 CACCAAGCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:862250 original size:29 final size:29
Alignment explanation
Indices: 862208--862265 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
862198 TGGTACTTAG
862208 TTCCTGGGTTCATGTTCATGATGATCAGC
1 TTCCTGGGTTCATGTTCATGATGATCAGC
862237 TTCCTGGGTTCATGTTCATGATGATCAGC
1 TTCCTGGGTTCATGTTCATGATGATCAGC
862266 CTGAGTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (29 bp):
TTCCTGGGTTCATGTTCATGATGATCAGC
Found at i:862709 original size:5 final size:5
Alignment explanation
Indices: 862691--862726 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
862681 CGAAGTACTC
862691 CCTC- CCTC- CCTCT CCTCT CCTCT CCTCT CCTCT CCT
1 CCTCT CCTCT CCTCT CCTCT CCTCT CCTCT CCTCT CCT
862727 ACTTCCCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 8 0.26
5 23 0.74
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (5 bp):
CCTCT
Found at i:880284 original size:2 final size:2
Alignment explanation
Indices: 880277--880310 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
880267 AACTTAACAG
*
880277 CT CT CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
880311 GTTTTCTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:880842 original size:2 final size:2
Alignment explanation
Indices: 880835--880861 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
880825 CAAAGTCTGA
880835 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
880862 ATGCGGCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:882804 original size:17 final size:18
Alignment explanation
Indices: 882782--882820 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
882772 AATTCATTTA
882782 TTTATTTATTATT-AAAT
1 TTTATTTATTATTAAAAT
*
882799 TTTA-TTATTTTTAAAAT
1 TTTATTTATTATTAAAAT
882816 TTTAT
1 TTTAT
882821 ACTGTTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATTTATTATTAAAAT
Found at i:884016 original size:21 final size:23
Alignment explanation
Indices: 883963--884017 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 23
883953 TTTTAAAAAG
* *
883963 TAATATTTAAAATGAATAATATTT
1 TAATATTAAAAATG-ATAATATTA
*
883987 TATTATTAAAAATG-TAA-ATTA
1 TAATATTAAAAATGATAATATTA
884008 TAATATTAAA
1 TAATATTAAA
884018 TAATATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 12 0.44
22 3 0.11
24 12 0.44
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
TAATATTAAAAATGATAATATTA
Found at i:893666 original size:34 final size:36
Alignment explanation
Indices: 893590--893666 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 36
893580 AAAAATATTG
* * *
893590 TTGATGAGAATATGCAACATATTAAGTATCTGAAAG
1 TTGAAGAGAATATACAACATATTAAGTATCTGAAAC
* *
893626 TCGAAGAGAATATACAATA-ATTAA-TATCTGAAAC
1 TTGAAGAGAATATACAACATATTAAGTATCTGAAAC
893660 TTGAAGA
1 TTGAAGA
893667 ACCTATAACC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 15 0.43
35 5 0.14
36 15 0.43
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.29
Consensus pattern (36 bp):
TTGAAGAGAATATACAACATATTAAGTATCTGAAAC
Found at i:894204 original size:21 final size:21
Alignment explanation
Indices: 894178--894219 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
894168 AAATAACAAG
894178 CTCAGCCCTCATTATTAAGCT
1 CTCAGCCCTCATTATTAAGCT
894199 CTCAGCCCTCATTATTAAGCT
1 CTCAGCCCTCATTATTAAGCT
894220 TTGAATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.33, G:0.10, T:0.33
Consensus pattern (21 bp):
CTCAGCCCTCATTATTAAGCT
Found at i:901583 original size:16 final size:16
Alignment explanation
Indices: 901562--901597 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
901552 CATTAGTGTA
*
901562 ACATATGACAATCTTG
1 ACATATGACAATATTG
*
901578 ACATATGAGAATATTG
1 ACATATGACAATATTG
901594 ACAT
1 ACAT
901598 GTAGATTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (16 bp):
ACATATGACAATATTG
Found at i:908037 original size:26 final size:27
Alignment explanation
Indices: 908008--908063 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
907998 TAAATTTTTA
*
908008 TATTTTTATTTTAAATTAAATAAGT-T
1 TATTTTTATTTTAAATCAAATAAGTCT
*
908034 TATTTTTATTTTAAATCACATAAGTCT
1 TATTTTTATTTTAAATCAAATAAGTCT
908061 TAT
1 TAT
908064 AATTAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 23 0.85
27 4 0.15
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (27 bp):
TATTTTTATTTTAAATCAAATAAGTCT
Found at i:910351 original size:2 final size:2
Alignment explanation
Indices: 910344--910389 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
910334 AATACCAATA
910344 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
910386 AT AT
1 AT AT
910390 CCTACCAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:915981 original size:27 final size:27
Alignment explanation
Indices: 915953--916048 Score: 82
Period size: 26 Copynumber: 3.9 Consensus size: 27
915943 GATACTTTTA
*
915953 AAAAGTGAATGAATA-TTTTATTTATT
1 AAAAGTGAATGAATACTTTTATCTATT
* *
915979 -AAA-T--A--AATATTTTTATCCATT
1 AAAAGTGAATGAATACTTTTATCTATT
* * *
916000 AAAAGTG-ATGAATATTTTTATGTATC
1 AAAAGTGAATGAATACTTTTATCTATT
916026 AAAAGTGAATGAATACTTTTATC
1 AAAAGTGAATGAATACTTTTATC
916049 CACTAGAAGC
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
20 4 0.07
21 9 0.16
22 4 0.07
23 1 0.02
24 2 0.04
25 3 0.05
26 20 0.36
27 13 0.23
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.43
Consensus pattern (27 bp):
AAAAGTGAATGAATACTTTTATCTATT
Found at i:916020 original size:26 final size:27
Alignment explanation
Indices: 915984--916050 Score: 91
Period size: 26 Copynumber: 2.5 Consensus size: 27
915974 TTATTAAATA
*
915984 AATATTTTTATCCATTAAAAGTG-ATG
1 AATATTTTTATCCATCAAAAGTGAATG
**
916010 AATATTTTTATGTATCAAAAGTGAATG
1 AATATTTTTATCCATCAAAAGTGAATG
*
916037 AATACTTTTATCCA
1 AATATTTTTATCCA
916051 CTAGAAGCAG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 20 0.59
27 14 0.41
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (27 bp):
AATATTTTTATCCATCAAAAGTGAATG
Found at i:916489 original size:14 final size:15
Alignment explanation
Indices: 916470--916498 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
916460 ATTAATTTAG
916470 TTTGATT-TTTCAAT
1 TTTGATTATTTCAAT
916484 TTTGATTATTTCAAT
1 TTTGATTATTTCAAT
916499 CAATTTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (15 bp):
TTTGATTATTTCAAT
Found at i:925643 original size:43 final size:43
Alignment explanation
Indices: 925582--925668 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
925572 TAGCTTTGCC
*
925582 GTTCGCCAACAGGTCGTGCAACGGTTCCTTGGGGAAAGGTGGG
1 GTTCGCCAACAAGTCGTGCAACGGTTCCTTGGGGAAAGGTGGG
925625 GTTCGCCAACAAGTCGTGCAACGGTTCCTTGGGGAAAGGTGGG
1 GTTCGCCAACAAGTCGTGCAACGGTTCCTTGGGGAAAGGTGGG
925668 G
1 G
925669 GAACGAAAGG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.20, C:0.21, G:0.39, T:0.21
Consensus pattern (43 bp):
GTTCGCCAACAAGTCGTGCAACGGTTCCTTGGGGAAAGGTGGG
Found at i:929081 original size:22 final size:22
Alignment explanation
Indices: 929033--929089 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
929023 TATTCTTATT
* * *
929033 TTTTATATTA-GAAGAATTGAA
1 TTTTATATTATAAAAAATTAAA
929054 TATTTATATTATAAAAAATTAAA
1 T-TTTATATTATAAAAAATTAAA
929077 TTTTA-A-TATAAAA
1 TTTTATATTATAAAA
929090 CATATTTAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 7 0.23
21 2 0.06
22 13 0.42
23 9 0.29
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (22 bp):
TTTTATATTATAAAAAATTAAA
Found at i:937070 original size:93 final size:93
Alignment explanation
Indices: 936911--937097 Score: 374
Period size: 93 Copynumber: 2.0 Consensus size: 93
936901 AAATTCAATG
936911 CATCCATTGTTTAACAATACAAAACAAAGCACGTCAAAGACCTTAATTCATGCATTTATCCTCAA
1 CATCCATTGTTTAACAATACAAAACAAAGCACGTCAAAGACCTTAATTCATGCATTTATCCTCAA
936976 ATCAGGTGAGAATTATAGATTTCCTAAA
66 ATCAGGTGAGAATTATAGATTTCCTAAA
937004 CATCCATTGTTTAACAATACAAAACAAAGCACGTCAAAGACCTTAATTCATGCATTTATCCTCAA
1 CATCCATTGTTTAACAATACAAAACAAAGCACGTCAAAGACCTTAATTCATGCATTTATCCTCAA
937069 ATCAGGTGAGAATTATAGATTTCCTAAA
66 ATCAGGTGAGAATTATAGATTTCCTAAA
937097 C
1 C
937098 GAAGAACTTG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.29
Consensus pattern (93 bp):
CATCCATTGTTTAACAATACAAAACAAAGCACGTCAAAGACCTTAATTCATGCATTTATCCTCAA
ATCAGGTGAGAATTATAGATTTCCTAAA
Found at i:939205 original size:7 final size:7
Alignment explanation
Indices: 939193--939231 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
939183 AGTAACACGG
939193 AGTCTCA
1 AGTCTCA
939200 AGTCTCA
1 AGTCTCA
939207 AGTCTCA
1 AGTCTCA
939214 AG--TCA
1 AGTCTCA
939219 AGTCTCA
1 AGTCTCA
939226 AGTCTC
1 AGTCTC
939232 TATCAATTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.17
7 25 0.83
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (7 bp):
AGTCTCA
Found at i:939221 original size:12 final size:12
Alignment explanation
Indices: 939193--939229 Score: 56
Period size: 12 Copynumber: 2.9 Consensus size: 12
939183 AGTAACACGG
939193 AGTCTCAAGTCTCA
1 AGTCTCAAG--TCA
939207 AGTCTCAAGTCA
1 AGTCTCAAGTCA
939219 AGTCTCAAGTC
1 AGTCTCAAGTC
939230 TCTATCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 14 0.61
14 9 0.39
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (12 bp):
AGTCTCAAGTCA
Found at i:945833 original size:126 final size:129
Alignment explanation
Indices: 945693--945930 Score: 297
Period size: 130 Copynumber: 1.8 Consensus size: 129
945683 TAACAACGAT
* * * ** *
945693 CAAGGTTATTAACTATTAGGAGGCGAGTAGGTCA-CTT-ATC-ACATATCAACCGATAATCTCCT
1 CAAGGCTATTAACTAGTAGGAAGCGAGTAAAT-AGCTTGATCAACATATCAACCGACAATCTCCT
* *
945755 TTTGAAATAATTTTTGTATATAACAT-ATATGA-ATTAAGTATAATGTGAATTAATAATAAATGA
65 TTTGAAACAATTTTTATATATAACATAATAT-ATATTAAGTATAATGTGAATTAATAATAAATGA
945818 G
129 G
* * *
945819 CAAGGCTATTAACTAGTAGGAAGCGAGTAAATAGCTTGATCGTAACATGTCAATCGACAATCTTC
1 CAAGGCTATTAACTAGTAGGAAGCGAGTAAATAGCTTGATC--AACATATCAACCGACAATCTCC
945884 TTTTGAAACAATTTTTATATATAACATGAATATATATTAAGTATAAT
64 TTTTGAAACAATTTTTATATATAACAT-AATATATATTAAGTATAAT
945931 AAGTGAGATT
Statistics
Matches: 93, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
125 1 0.01
126 30 0.32
127 3 0.03
130 42 0.45
131 1 0.01
132 16 0.17
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (129 bp):
CAAGGCTATTAACTAGTAGGAAGCGAGTAAATAGCTTGATCAACATATCAACCGACAATCTCCTT
TTGAAACAATTTTTATATATAACATAATATATATTAAGTATAATGTGAATTAATAATAAATGAG
Found at i:946000 original size:111 final size:113
Alignment explanation
Indices: 945863--946139 Score: 303
Period size: 111 Copynumber: 2.5 Consensus size: 113
945853 CTTGATCGTA
* * * *
945863 ACATGTCAATCGACAATCTTCTTTTGAAACAATTTTTATATATAACAT-GAATATATATTAAGTA
1 ACATGTCAATTGATAATCTCCTTTTGAAACAATTTTTATATATAACATAG-ATATAAATTAAGTA
* * * * * * *
945927 T-AATAAGTGAGATTATTAATTATTAGTA-GACGAAAAAATGACT-TGTT
65 TAAATAAGCGAGATTATTAACTATTA-AAGGAAGAAAAAATAACTCAGTC
* * ** *
945974 ACATGTCAATTAATAATCTCCTTTTGAAACAATATTTATATATAGTATAGATATAAATTAAGTGT
1 ACATGTCAATTGATAATCTCCTTTTGAAACAATTTTTATATATAACATAGATATAAATTAAGTAT
* *
946039 AAATGAGCGAGATTATTAACTATTAAAGGAAGAGAAAATAACTCAGTC
66 AAATAAGCGAGATTATTAACTATTAAAGGAAGAAAAAATAACTCAGTC
* ** *
946087 ACATGTCAATTGATAATCTCCCTTCAAAACAA-TTTTATATATAATATAGATAT
1 ACATGTCAATTGATAATCTCCTTTTGAAACAATTTTTATATATAACATAGATAT
946140 GAGATGCGAA
Statistics
Matches: 138, Mismatches: 24, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
111 55 0.40
112 53 0.38
113 30 0.22
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (113 bp):
ACATGTCAATTGATAATCTCCTTTTGAAACAATTTTTATATATAACATAGATATAAATTAAGTAT
AAATAAGCGAGATTATTAACTATTAAAGGAAGAAAAAATAACTCAGTC
Found at i:946135 original size:112 final size:110
Alignment explanation
Indices: 945889--946139 Score: 281
Period size: 112 Copynumber: 2.2 Consensus size: 110
945879 TCTTCTTTTG
* * * *
945889 AAACAATTTTTATATATAACAT-GAATATATATTAAGTATAATAAGTGAGATTATTAATTATTAG
1 AAACAA-TTTTATATATAATATAG-ATATAAATTAAGTATAATAAGCGAGATTATTAACTATTAG
* * * * * * **
945953 TAGACGAAAAAATGACTTGTTACATGTCAATTAATAATCTCCTTTTG
64 AAGAAGAAAAAATAACTAGTCACATGTCAATTAATAATCTCCCTTCA
* * *
946000 AAACAATATTTATATATAGTATAGATATAAATTAAGTGTAAATGAGCGAGATTATTAACTATTA-
1 AAACAAT-TTTATATATAATATAGATATAAATTAAGTAT-AATAAGCGAGATTATTAACTATTAG
* *
946064 AAGGAAGAGAAAATAACTCAGTCACATGTCAATTGATAATCTCCCTTCA
64 AA-GAAGAAAAAATAACT-AGTCACATGTCAATTAATAATCTCCCTTCA
946113 AAACAATTTTATATATAATATAGATAT
1 AAACAATTTTATATATAATATAGATAT
946140 GAGATGCGAA
Statistics
Matches: 117, Mismatches: 18, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
110 1 0.01
111 32 0.27
112 53 0.45
113 31 0.26
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.35
Consensus pattern (110 bp):
AAACAATTTTATATATAATATAGATATAAATTAAGTATAATAAGCGAGATTATTAACTATTAGAA
GAAGAAAAAATAACTAGTCACATGTCAATTAATAATCTCCCTTCA
Found at i:957985 original size:94 final size:95
Alignment explanation
Indices: 957824--958004 Score: 265
Period size: 94 Copynumber: 1.9 Consensus size: 95
957814 ATCCAAATCG
* * * * *
957824 AGAAAAAAAATCATAGAGAACATTATTGTTGATAGACAAAGTATATAGTTTGGCTGTCTCTATCA
1 AGAAAAAAAATCATAGAGAACATCATTGTTGATAGACAAAGGAGATAGCTTGGCTGTCTCTAGCA
957889 AATTTTAAGGTT-TTAACTTATCAAAATAA
66 AATTTTAAGGTTATTAACTTATCAAAATAA
* * * * *
957918 AGAAAAGAAATTATAGAGGACATCATTGTTGGTAGACAAAGGAGATAGCTTGGCTGTTTCTAGCA
1 AGAAAAAAAATCATAGAGAACATCATTGTTGATAGACAAAGGAGATAGCTTGGCTGTCTCTAGCA
957983 AATTTTAAGGTTATTAACTTAT
66 AATTTTAAGGTTATTAACTTAT
958005 TTGATTAGGG
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
94 67 0.88
95 9 0.12
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (95 bp):
AGAAAAAAAATCATAGAGAACATCATTGTTGATAGACAAAGGAGATAGCTTGGCTGTCTCTAGCA
AATTTTAAGGTTATTAACTTATCAAAATAA
Found at i:964141 original size:15 final size:16
Alignment explanation
Indices: 964118--964153 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
964108 TTTGTAGGAT
964118 TCTTT-TTTAAT-AAA
1 TCTTTCTTTAATGAAA
964132 TCTTTCTTTAATGAAA
1 TCTTTCTTTAATGAAA
964148 TCTTTC
1 TCTTTC
964154 ATTTGTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 5 0.25
15 6 0.30
16 9 0.45
ACGTcount: A:0.28, C:0.14, G:0.03, T:0.56
Consensus pattern (16 bp):
TCTTTCTTTAATGAAA
Found at i:969386 original size:110 final size:111
Alignment explanation
Indices: 969248--969468 Score: 268
Period size: 111 Copynumber: 2.0 Consensus size: 111
969238 TAGCAGTGTG
**
969248 CTTTAACTTCTTATAATCATATAATTCAAACCCAAAC-AAAAGAATTAAT-ATTTCGA-TATGGA
1 CTTTAACTTCTTATAATCATATAATTCAAACCCAAACAAAAAG-A-TAATCATTTCGATTACAGA
* * * * *
969310 AATCATCAAATTAATGGATCTCGATAAAAAATTGTGACAATCTATAAC
64 AATCATCAAATTAATAGATCTCAACAAAAAATTGTAACAATCAATAAC
** *** * *
969358 CTTTAACTTCTTATAATCATATGTTTCAAATTTAAATAAAAAGATCATCATTTCGATTACAGAAA
1 CTTTAACTTCTTATAATCATATAATTCAAACCCAAACAAAAAGATAATCATTTCGATTACAGAAA
*
969423 TCATCAAATTAATAGATCTCAACAAAAAGTTGTAACAATCAATAAC
66 TCATCAAATTAATAGATCTCAACAAAAAATTGTAACAATCAATAAC
969469 AGTGTGCTTT
Statistics
Matches: 93, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
109 3 0.03
110 39 0.42
111 51 0.55
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (111 bp):
CTTTAACTTCTTATAATCATATAATTCAAACCCAAACAAAAAGATAATCATTTCGATTACAGAAA
TCATCAAATTAATAGATCTCAACAAAAAATTGTAACAATCAATAAC
Found at i:979098 original size:4 final size:4
Alignment explanation
Indices: 979091--979116 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
979081 TATAAATAAA
979091 TAAT TAAT TAAT TAAT TAAT TAAT TA
1 TAAT TAAT TAAT TAAT TAAT TAAT TA
979117 TAAATTTCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:1006880 original size:20 final size:20
Alignment explanation
Indices: 1006855--1006896 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1006845 CCAGGTCCCG
1006855 CGTTCGAATCTAGACTCTCC
1 CGTTCGAATCTAGACTCTCC
1006875 CGTTCGAATCTAGACTCTCC
1 CGTTCGAATCTAGACTCTCC
1006895 CG
1 CG
1006897 ACAGGGGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.36, G:0.17, T:0.29
Consensus pattern (20 bp):
CGTTCGAATCTAGACTCTCC
Found at i:1024008 original size:43 final size:43
Alignment explanation
Indices: 1023946--1024042 Score: 160
Period size: 43 Copynumber: 2.3 Consensus size: 43
1023936 AAATGGTAAT
1023946 ACATTTCAGCCACAGAACACAAGAAAAAAGGTGAAGTGGCAAC
1 ACATTTCAGCCACAGAACACAAGAAAAAAGGTGAAGTGGCAAC
* * *
1023989 ACATTTCAGGCACATAACACAATAAAAAAGGTGAAGTGGCAAC
1 ACATTTCAGCCACAGAACACAAGAAAAAAGGTGAAGTGGCAAC
1024032 ACA-TTCAGCCA
1 ACATTTCAGCCA
1024043 GGTGAAGGGG
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 7 0.14
43 43 0.86
ACGTcount: A:0.45, C:0.22, G:0.19, T:0.14
Consensus pattern (43 bp):
ACATTTCAGCCACAGAACACAAGAAAAAAGGTGAAGTGGCAAC
Found at i:1026539 original size:17 final size:17
Alignment explanation
Indices: 1026513--1026545 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1026503 GTTAATAAAT
1026513 AAATTTAAAAA-AATAC
1 AAATTTAAAAAGAATAC
1026529 AAATCTTAAAAAGAATA
1 AAAT-TTAAAAAGAATA
1026546 AATATCCCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.24
Consensus pattern (17 bp):
AAATTTAAAAAGAATAC
Found at i:1045307 original size:21 final size:21
Alignment explanation
Indices: 1045278--1045317 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1045268 TAAAATTAAA
* *
1045278 AAATTAATTACTTTTAAATAT
1 AAATAAATTAATTTTAAATAT
1045299 AAATAAATTAATTTTAAAT
1 AAATAAATTAATTTTAAAT
1045318 TACAAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATAAATTAATTTTAAATAT
Found at i:1045333 original size:22 final size:21
Alignment explanation
Indices: 1045278--1045325 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1045268 TAAAATTAAA
* * *
1045278 AAATTAATTACTTTTAAATAT
1 AAATAAATTAATTTTAAATAC
1045299 AAATAAATTAATTTTAAATTAC
1 AAATAAATTAATTTTAAA-TAC
1045321 AAATA
1 AAATA
1045326 TTTTAATTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATAAATTAATTTTAAATAC
Found at i:1045804 original size:20 final size:19
Alignment explanation
Indices: 1045781--1045837 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
1045771 TAGAATATTC
1045781 ATTTATAAATTTGAATAACA
1 ATTTATAAATTTGAATAA-A
* *
1045801 ATTTA-AAATTTTAATTGAAT
1 ATTTATAAATTTGAA-T-AAA
1045821 ATTTATAAATTTGAATA
1 ATTTATAAATTTGAATA
1045838 TGTTATCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 9 0.29
20 12 0.39
21 10 0.32
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (19 bp):
ATTTATAAATTTGAATAAA
Found at i:1045836 original size:16 final size:18
Alignment explanation
Indices: 1045815--1045848 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1045805 AAAATTTTAA
1045815 TTGAATAT-TTAT-AAAT
1 TTGAATATGTTATCAAAT
1045831 TTGAATATGTTATCAAAT
1 TTGAATATGTTATCAAAT
1045849 ATTAGTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 4 0.25
18 4 0.25
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (18 bp):
TTGAATATGTTATCAAAT
Found at i:1046003 original size:70 final size:69
Alignment explanation
Indices: 1045870--1046004 Score: 157
Period size: 70 Copynumber: 1.9 Consensus size: 69
1045860 TTTAAAATGA
* * *
1045870 AAAGTTGTCACTTAATAATGTAACTATTAAAAAAACACATTTAATGAAAAAGTTATGTCTTATAA
1 AAAGTTGTCACTTAACAATGTAACTATTAAAAAAACACATTTAATCAAAAAGTTATATCTTATAA
1045935 TATT
66 TATT
* * * * *
1045939 AAAGATTGTCACTTAACAATGTGATTATTGAAAAAATAC-TTATAATCCAAAAA-TTATATTTTA
1 AAAG-TTGTCACTTAACAATGTAACTATTAAAAAAACACATT-TAAT-CAAAAAGTTATATCTTA
1046002 TAA
63 TAA
1046005 CTGCAACGCT
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
69 6 0.11
70 44 0.80
71 5 0.09
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (69 bp):
AAAGTTGTCACTTAACAATGTAACTATTAAAAAAACACATTTAATCAAAAAGTTATATCTTATAA
TATT
Found at i:1050795 original size:16 final size:15
Alignment explanation
Indices: 1050769--1050815 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
1050759 GTAAAAATAA
*
1050769 TAAATATAATTTTAAT
1 TAAAAATAA-TTTAAT
*
1050785 TAATAATAA-TTAAT
1 TAAAAATAATTTAAT
1050799 TAAAAATTAATTTAAT
1 TAAAAA-TAATTTAAT
1050815 T
1 T
1050816 TAAATATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 10 0.38
15 3 0.12
16 13 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAAAATAATTTAAT
Found at i:1052280 original size:19 final size:19
Alignment explanation
Indices: 1052252--1052294 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
1052242 GGTTTCATTA
* *
1052252 AAATAATATTTTTTAATTT
1 AAATAATATTGTATAATTT
* *
1052271 TAATAGTATTGTATAATTT
1 AAATAATATTGTATAATTT
1052290 AAATA
1 AAATA
1052295 TAAATATTTT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
AAATAATATTGTATAATTT
Found at i:1062410 original size:13 final size:12
Alignment explanation
Indices: 1062379--1062410 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
1062369 TTATATAATT
1062379 TATTTTATCAAA
1 TATTTTATCAAA
1062391 TATTTTATCAAA
1 TATTTTATCAAA
1062403 TAATTTTA
1 T-ATTTTA
1062411 ACTTAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (12 bp):
TATTTTATCAAA
Found at i:1065103 original size:15 final size:16
Alignment explanation
Indices: 1065078--1065108 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1065068 CTTCGTCAAA
1065078 AAATGATAATTCTTTT
1 AAATGATAATTCTTTT
1065094 AAAT-ATAATTCTTTT
1 AAATGATAATTCTTTT
1065109 CTATTGCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (16 bp):
AAATGATAATTCTTTT
Found at i:1068200 original size:22 final size:20
Alignment explanation
Indices: 1068157--1068205 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
1068147 TGTTTTTTAA
**
1068157 AAATAAAAATTTTAAATTTT
1 AAATAAAAATTTTAAAAATT
1068177 AAATAAAATATTTTTAAAAATT
1 AAATAAAA-A-TTTTAAAAATT
1068199 AAA-AAAA
1 AAATAAAA
1068206 CTACAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.32
21 5 0.20
22 12 0.48
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATAAAAATTTTAAAAATT
Found at i:1072208 original size:19 final size:20
Alignment explanation
Indices: 1072167--1072222 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
1072157 AATTTTTTTA
1072167 TAAATATTTATAATTAAGTT
1 TAAATATTTATAATTAAGTT
*
1072187 TAAATA-TTATTAATTTAGTT
1 TAAATATTTA-TAATTAAGTT
* * *
1072207 AAAATGTATATAATTA
1 TAAATATTTATAATTA
1072223 GATTTTAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.10
20 24 0.83
21 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48
Consensus pattern (20 bp):
TAAATATTTATAATTAAGTT
Found at i:1080413 original size:2 final size:2
Alignment explanation
Indices: 1080406--1080431 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1080396 GACAGCATCA
1080406 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
1080432 GTGCAAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1084212 original size:19 final size:19
Alignment explanation
Indices: 1084167--1084212 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1084157 GAGTGATTTG
*
1084167 TATTTAAATATTTAATTTAT
1 TATTT-AATATATAATTTAT
* *
1084187 TAATTAATATATAATTTTT
1 TATTTAATATATAATTTAT
1084206 TATTTAA
1 TATTTAA
1084213 AAAGTAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTTAATATATAATTTAT
Found at i:1101550 original size:2 final size:2
Alignment explanation
Indices: 1101543--1101572 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1101533 CCTCTACTAA
1101543 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1101573 GTTATACACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1111711 original size:194 final size:193
Alignment explanation
Indices: 1111372--1111759 Score: 643
Period size: 194 Copynumber: 2.0 Consensus size: 193
1111362 ATTTTTCAGA
* *
1111372 TGGAAGTTTTGTTTGAAGCAAGAAGATTGAATTTAAAGATTTTGGTCTCGATAGAACTTTGACAT
1 TGGAAGTTTTGTTTGAAGCAAGAAGATTGAATTTAAAGATTTTGGTATCAATAGAACTTTGACAT
*
1111437 GTCTCTTCTCCACCCACATTAATGTATTACTGGTTAAAAAAATTAGGGACCTTTTTTCATGAGCC
66 GTCTCTTCTCCACCCACATTAATGTATTACTGGTTAAAAAAATTAGGGACCTTTTTCCATGAGCC
* * * * * *
1111502 TTTCATTATGTAACATTTCTTTTTCCATGAATAGAGGTAAAGACAATATGATATTGCTGAACT
131 TTTCATGAAGTAACATTTCCTTTTACATGAATAAAGCTAAAGACAATATGATATTGCTGAACT
**
1111565 TGGAAGTTTTTGTTTGAAGCAAGAAGATTGAATTTAAAGATTTTGGTATCAATAGAACTTTGATG
1 TGGAAG-TTTTGTTTGAAGCAAGAAGATTGAATTTAAAGATTTTGGTATCAATAGAACTTTGACA
*
1111630 TGTCTCTTCTCCACCCACATTAATGTATTACTGGTTGAAAAAATTAGGGA-CTTTTTCCCATGAG
65 TGTCTCTTCTCCACCCACATTAATGTATTACTGGTTAAAAAAATTAGGGACCTTTTT-CCATGAG
1111694 CCTTTCATGAAGTAACATTTCCTTTTACATGAATAAAGCTAAAGACAATATGATATTGCTGAACT
129 CCTTTCATGAAGTAACATTTCCTTTTACATGAATAAAGCTAAAGACAATATGATATTGCTGAACT
1111759 T
1 T
1111760 TATTGGAATC
Statistics
Matches: 181, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
193 12 0.07
194 169 0.93
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (193 bp):
TGGAAGTTTTGTTTGAAGCAAGAAGATTGAATTTAAAGATTTTGGTATCAATAGAACTTTGACAT
GTCTCTTCTCCACCCACATTAATGTATTACTGGTTAAAAAAATTAGGGACCTTTTTCCATGAGCC
TTTCATGAAGTAACATTTCCTTTTACATGAATAAAGCTAAAGACAATATGATATTGCTGAACT
Found at i:1118282 original size:6 final size:6
Alignment explanation
Indices: 1118271--1118326 Score: 76
Period size: 6 Copynumber: 9.3 Consensus size: 6
1118261 CAAAGATTTT
* * * *
1118271 GTTTGA GTTTGA GCTTGA GCTTGA GCTAGA GTTTGA GTTTGA GTTTGA
1 GTTTGA GTTTGA GTTTGA GTTTGA GTTTGA GTTTGA GTTTGA GTTTGA
1118319 GTTTGA GT
1 GTTTGA GT
1118327 GCTGTGAGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.18, C:0.05, G:0.34, T:0.43
Consensus pattern (6 bp):
GTTTGA
Found at i:1125593 original size:23 final size:24
Alignment explanation
Indices: 1125567--1125611 Score: 58
Period size: 22 Copynumber: 1.9 Consensus size: 24
1125557 TTAAACATAT
*
1125567 ATGAGTTTATTTA-ATA-AAAAATC
1 ATGA-TTTAATTACATATAAAAATC
1125590 ATGATTTAATTACATATAAAAA
1 ATGATTTAATTACATATAAAAA
1125612 GATTAGGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 7 0.37
24 5 0.26
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (24 bp):
ATGATTTAATTACATATAAAAATC
Found at i:1126159 original size:16 final size:17
Alignment explanation
Indices: 1126133--1126164 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1126123 ACCATATGTA
1126133 CAAATTAAAATTTTAAT
1 CAAATTAAAATTTTAAT
1126150 CAAA-TAAAATTTTAA
1 CAAATTAAAATTTTAA
1126165 ATTCTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
CAAATTAAAATTTTAAT
Found at i:1163551 original size:28 final size:31
Alignment explanation
Indices: 1163510--1163577 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
1163500 CTCCTTATGG
*
1163510 AAACAAAAATTATCCAT-A-ATATTAATTGA
1 AAACAAAAATTATCCATAAGATATTAATAGA
*
1163539 AAACAAAAA-TATCGATAAGATATTAATAGA
1 AAACAAAAATTATCCATAAGATATTAATAGA
*
1163569 AAAAAAAAA
1 AAACAAAAA
1163578 CAAATCACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 6 0.18
29 10 0.29
30 18 0.53
ACGTcount: A:0.63, C:0.07, G:0.06, T:0.24
Consensus pattern (31 bp):
AAACAAAAATTATCCATAAGATATTAATAGA
Found at i:1166454 original size:13 final size:13
Alignment explanation
Indices: 1166438--1166463 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1166428 GTATGTTACC
1166438 TTTGAGATGGAAG
1 TTTGAGATGGAAG
1166451 TTTGAGATGGAAG
1 TTTGAGATGGAAG
1166464 GATGAGCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.38, T:0.31
Consensus pattern (13 bp):
TTTGAGATGGAAG
Found at i:1177756 original size:19 final size:20
Alignment explanation
Indices: 1177719--1177757 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1177709 AAACATCAAC
*
1177719 TTTTTCCTTTTAACTACAAG
1 TTTTTCCTTTTAACAACAAG
*
1177739 TTTTT-CTTTTACCAACAAG
1 TTTTTCCTTTTAACAACAAG
1177758 AAGTCAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.49
Consensus pattern (20 bp):
TTTTTCCTTTTAACAACAAG
Found at i:1178730 original size:30 final size:31
Alignment explanation
Indices: 1178679--1178752 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 31
1178669 ATAAAATAAT
* * *
1178679 AAATAATAT-TTTAATTAATTATTAAT-TATA
1 AAATAATATATTAAAATAATTA-TAATAAATA
1178709 AAATAATATATTAAAAT-ATTATAATAAATA
1 AAATAATATATTAAAATAATTATAATAAATA
*
1178739 AAATATTATATTAA
1 AAATAATATATTAA
1178753 TATTATATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 4 0.11
30 29 0.76
31 5 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (31 bp):
AAATAATATATTAAAATAATTATAATAAATA
Found at i:1187766 original size:31 final size:30
Alignment explanation
Indices: 1187731--1187792 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
1187721 ATATTAACCA
* * * *
1187731 TTAAAGTAGAGGGATTAAATTATTTTAATTT
1 TTAAAATAGAGAGATT-AATTAATTAAATTT
*
1187762 TTAAAATTGAGAGATTAATTAATTAAATTT
1 TTAAAATAGAGAGATTAATTAATTAAATTT
1187792 T
1 T
1187793 AAATACATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (30 bp):
TTAAAATAGAGAGATTAATTAATTAAATTT
Found at i:1189230 original size:21 final size:21
Alignment explanation
Indices: 1189181--1189230 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1189171 GTAAATATAA
1189181 AATATTAATAATTATATAAAT
1 AATATTAATAATTATATAAAT
*
1189202 AA-ATTTAATTAATTATAT-TAT
1 AATA-TTAA-TAATTATATAAAT
1189223 AATATTAA
1 AATATTAA
1189231 ATACCTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 1 0.04
21 14 0.56
22 10 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATATTAATAATTATATAAAT
Found at i:1189771 original size:14 final size:15
Alignment explanation
Indices: 1189752--1189780 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1189742 GTGTCTTGCC
1189752 TTTTTT-CTTTTTTT
1 TTTTTTCCTTTTTTT
1189766 TTTTTTCCTTTTTTT
1 TTTTTTCCTTTTTTT
1189781 GAAGGAAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTCCTTTTTTT
Found at i:1206600 original size:18 final size:18
Alignment explanation
Indices: 1206577--1206620 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
1206567 TTATTTTGAT
1206577 ATTATTTTATAATAAATC
1 ATTATTTTATAATAAATC
*
1206595 ATTATTTTATCATAAATC
1 ATTATTTTATAATAAATC
1206613 ATTATTTT
1 ATTATTTT
1206621 TTTTAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTATTTTATAATAAATC
Found at i:1208728 original size:21 final size:21
Alignment explanation
Indices: 1208703--1208742 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1208693 GGTGAGGCCT
1208703 GCAAATGCTGAACAATATCCC
1 GCAAATGCTGAACAATATCCC
1208724 GCAAATGCTGAACAATATC
1 GCAAATGCTGAACAATATC
1208743 TCACAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.20
Consensus pattern (21 bp):
GCAAATGCTGAACAATATCCC
Found at i:1208749 original size:21 final size:21
Alignment explanation
Indices: 1208704--1208750 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1208694 GTGAGGCCTG
*
1208704 CAAATGCTGAACAATATCCCG
1 CAAATGCTGAACAATATCCCA
*
1208725 CAAATGCTGAACAATATCTCA
1 CAAATGCTGAACAATATCCCA
1208746 CAAAT
1 CAAAT
1208751 TCCGTTGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.21
Consensus pattern (21 bp):
CAAATGCTGAACAATATCCCA
Found at i:1211516 original size:18 final size:17
Alignment explanation
Indices: 1211475--1211519 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
1211465 TAAACCGAGG
1211475 AAGAGGAAAAGGTAGAA
1 AAGAGGAAAAGGTAGAA
1211492 AATGAGGTAAAA-GTAGAA
1 AA-GAGG-AAAAGGTAGAA
1211510 ATAGAGGAAA
1 A-AGAGGAAA
1211520 CCAAAATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 5 0.20
ACGTcount: A:0.58, C:0.00, G:0.31, T:0.11
Consensus pattern (17 bp):
AAGAGGAAAAGGTAGAA
Found at i:1212811 original size:15 final size:15
Alignment explanation
Indices: 1212791--1212820 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1212781 GGAGTGTGCA
1212791 TATTTTGAATAAAAG
1 TATTTTGAATAAAAG
1212806 TATTTTGAATAAAAG
1 TATTTTGAATAAAAG
1212821 CCCCACACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (15 bp):
TATTTTGAATAAAAG
Found at i:1216456 original size:7 final size:7
Alignment explanation
Indices: 1216444--1216476 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1216434 AACTGAAATT
1216444 ATTATTC
1 ATTATTC
1216451 ATTATTC
1 ATTATTC
*
1216458 ATTATTT
1 ATTATTC
1216465 ATTATT-
1 ATTATTC
1216471 ATTATT
1 ATTATT
1216477 AACATCACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (7 bp):
ATTATTC
Found at i:1220519 original size:27 final size:27
Alignment explanation
Indices: 1220487--1220608 Score: 127
Period size: 27 Copynumber: 4.5 Consensus size: 27
1220477 ATATGTCAAG
* * *
1220487 TTAAAAATTTAGTTATCATATATTATA
1 TTAAAAATTTAATTATTATATACTATA
* * *
1220514 TAAAAAAAATTAATTATTATATACCATA
1 T-TAAAAATTTAATTATTATATACTATA
* *
1220542 TTAAAAATTTAATTGTTATACACTATA
1 TTAAAAATTTAATTATTATATACTATA
* * *
1220569 TTAAAAATTTAATCATTACATACCATA
1 TTAAAAATTTAATTATTATATACTATA
*
1220596 TTGAAAATTTAAT
1 TTAAAAATTTAAT
1220609 ATCTACATCA
Statistics
Matches: 77, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
27 56 0.73
28 21 0.27
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.42
Consensus pattern (27 bp):
TTAAAAATTTAATTATTATATACTATA
Found at i:1220547 original size:55 final size:54
Alignment explanation
Indices: 1220487--1220615 Score: 145
Period size: 54 Copynumber: 2.4 Consensus size: 54
1220477 ATATGTCAAG
* * * * *
1220487 TTAAAAATTTAGTTATCATATATTATATAAAAAAAATTAATTATTATATACCATA
1 TTAAAAATTTAATTATCATACACTATAT-AAAAAAATTAATCATTACATACCATA
* * * *
1220542 TTAAAAATTTAATTGTTATACACTATATTAAAAATTTAATCATTACATACCATA
1 TTAAAAATTTAATTATCATACACTATATAAAAAAATTAATCATTACATACCATA
*
1220596 TTGAAAATTTAA-TATC-TACA
1 TTAAAAATTTAATTATCATACA
1220616 TCATGCGCGT
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
52 4 0.06
53 2 0.03
54 33 0.53
55 23 0.37
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (54 bp):
TTAAAAATTTAATTATCATACACTATATAAAAAAATTAATCATTACATACCATA
Found at i:1221742 original size:29 final size:29
Alignment explanation
Indices: 1221710--1221770 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
1221700 AGTTTTAACC
* *
1221710 AAAATTTTAAACGGATTCATTAGTTTTCG
1 AAAATTCTAAACAGATTCATTAGTTTTCG
1221739 AAAATTCTAAACAGATTCATTAGTTTTCG
1 AAAATTCTAAACAGATTCATTAGTTTTCG
1221768 AAA
1 AAA
1221771 TAAATATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.38
Consensus pattern (29 bp):
AAAATTCTAAACAGATTCATTAGTTTTCG
Found at i:1224348 original size:2 final size:2
Alignment explanation
Indices: 1224341--1224370 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1224331 CTACTTGCAC
1224341 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1224371 GTTGCTTGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1228437 original size:25 final size:25
Alignment explanation
Indices: 1228388--1228438 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1228378 AACTTCTAAG
*
1228388 CCCCTTGTAATTTGTGTTTACCCTT
1 CCCCTTGTAATTTGTGTTAACCCTT
*
1228413 CCCCTTGTAATTTGTGTTAATCCTT
1 CCCCTTGTAATTTGTGTTAACCCTT
1228438 C
1 C
1228439 TGGTTTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.14, C:0.27, G:0.12, T:0.47
Consensus pattern (25 bp):
CCCCTTGTAATTTGTGTTAACCCTT
Found at i:1229433 original size:4 final size:4
Alignment explanation
Indices: 1229424--1229450 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1229414 TATTTCCACA
1229424 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
1229451 CAACCCCCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:1232379 original size:2 final size:2
Alignment explanation
Indices: 1232372--1232398 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1232362 TCTGGAAGGA
1232372 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1232399 TGACTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1238343 original size:15 final size:16
Alignment explanation
Indices: 1238311--1238368 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 16
1238301 TTTTTATTTT
1238311 TTTAGTTTATATTATTA
1 TTTA-TTTATATTATTA
1238328 -TTATTTATA-TATTTA
1 TTTATTTATATTA-TTA
* *
1238343 TTTATTTCTATT-CTA
1 TTTATTTATATTATTA
*
1238358 TTTATTGATAT
1 TTTATTTATAT
1238369 GTTTTAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 2 0.06
15 20 0.59
16 11 0.32
17 1 0.03
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (16 bp):
TTTATTTATATTATTA
Found at i:1238775 original size:16 final size:17
Alignment explanation
Indices: 1238754--1238785 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1238744 TGACCCTCAA
1238754 AATAATT-TTTTTATTT
1 AATAATTATTTTTATTT
1238770 AATAATTATTTTTATT
1 AATAATTATTTTTATT
1238786 CTTCAAACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
AATAATTATTTTTATTT
Found at i:1241579 original size:19 final size:18
Alignment explanation
Indices: 1241552--1241587 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1241542 ATATCAAACA
1241552 GAAGAATAAAATAGATTAT
1 GAAGAATAAAATA-ATTAT
*
1241571 GAAGTATAAAATAATTA
1 GAAGAATAAAATAATTA
1241588 AATGTTGCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.58, C:0.00, G:0.14, T:0.28
Consensus pattern (18 bp):
GAAGAATAAAATAATTAT
Found at i:1245464 original size:16 final size:15
Alignment explanation
Indices: 1245426--1245468 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
1245416 GAAAAAGGAG
*
1245426 TTTTTTCAAAAAGTT
1 TTTTTTTAAAAAGTT
1245441 TTTTTTTAAAAA-TT
1 TTTTTTTAAAAAGTT
1245455 TTATTCTTTAAAAA
1 TT-TT-TTTAAAAA
1245469 AAACCTACTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 4 0.16
15 13 0.52
16 8 0.32
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (15 bp):
TTTTTTTAAAAAGTT
Found at i:1256333 original size:18 final size:18
Alignment explanation
Indices: 1256310--1256344 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1256300 GTATATTATT
*
1256310 TAATAATCAATCAAAAAG
1 TAATAATAAATCAAAAAG
*
1256328 TAATAATAAATTAAAAA
1 TAATAATAAATCAAAAA
1256345 TAGTGATAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
TAATAATAAATCAAAAAG
Found at i:1264669 original size:3 final size:3
Alignment explanation
Indices: 1264661--1264690 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1264651 TCAGGAGAAG
1264661 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1264691 CCCACGCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:1280583 original size:28 final size:29
Alignment explanation
Indices: 1280543--1280612 Score: 97
Period size: 28 Copynumber: 2.4 Consensus size: 29
1280533 GTATAAAATA
1280543 ATTTAAATAAATTTTTAT-TTTTTATTAT
1 ATTTAAATAAATTTTTATATTTTTATTAT
* *
1280571 ATTTAATTAAATTTTTATATTTTTATTTT
1 ATTTAAATAAATTTTTATATTTTTATTAT
*
1280600 AAATTAAATAAAT
1 -ATTTAAATAAAT
1280613 CATCATAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
28 17 0.47
29 9 0.25
30 10 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
ATTTAAATAAATTTTTATATTTTTATTAT
Found at i:1287868 original size:21 final size:21
Alignment explanation
Indices: 1287844--1287885 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1287834 AATGTTTTTT
* *
1287844 TTTTAAGTAAAGATATTTTAA
1 TTTTAAGTAAAAAAATTTTAA
*
1287865 TTTTAATTAAAAAAATTTTAA
1 TTTTAAGTAAAAAAATTTTAA
1287886 AAATTATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (21 bp):
TTTTAAGTAAAAAAATTTTAA
Found at i:1291359 original size:17 final size:17
Alignment explanation
Indices: 1291337--1291369 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1291327 TTCAATTAAC
1291337 CAAAATCAAAT-GATTTA
1 CAAAAT-AAATAGATTTA
1291354 CAAAATAAATAGATTT
1 CAAAATAAATAGATTT
1291370 CAATTATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (17 bp):
CAAAATAAATAGATTTA
Found at i:1317548 original size:34 final size:35
Alignment explanation
Indices: 1317509--1317578 Score: 90
Period size: 37 Copynumber: 2.0 Consensus size: 35
1317499 CAAAGATGCA
1317509 GGTTAACATT-T-AGTAAATAAAATCAAAGAGACAG
1 GGTTAACATTATAAGTAAAT-AAATCAAAGAGACAG
*
1317543 GGTTAACATTCAATAATTAAATAAATCAAAGAGACA
1 GGTTAACATT--ATAAGTAAATAAATCAAAGAGACA
1317579 ACAAAACAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
34 10 0.32
37 15 0.48
38 6 0.19
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.24
Consensus pattern (35 bp):
GGTTAACATTATAAGTAAATAAATCAAAGAGACAG
Found at i:1321465 original size:2 final size:2
Alignment explanation
Indices: 1321458--1321487 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1321448 TGTGCAGCAG
1321458 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1321488 TTGTTCACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1333915 original size:36 final size:36
Alignment explanation
Indices: 1333868--1333964 Score: 149
Period size: 36 Copynumber: 2.7 Consensus size: 36
1333858 ACCAACCTCA
1333868 ATGTGCACTCCCACATTGCACATAGCTATTATTGTT
1 ATGTGCACTCCCACATTGCACATAGCTATTATTGTT
* *
1333904 ATGTGCACTCCCACACTGCACATAGTTATTATTGTT
1 ATGTGCACTCCCACATTGCACATAGCTATTATTGTT
* * *
1333940 ATGTGCACTCTCACCTCGCACATAG
1 ATGTGCACTCCCACATTGCACATAG
1333965 TTATCATCAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.33
Consensus pattern (36 bp):
ATGTGCACTCCCACATTGCACATAGCTATTATTGTT
Found at i:1335543 original size:36 final size:36
Alignment explanation
Indices: 1335503--1335579 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
1335493 TCAATTCAGC
*
1335503 TCATGTGCACTCCCACACCACACATAGTTATCATCG
1 TCATGTGCACTCCCACACCACACATAGTTATCATCA
* ** *
1335539 TCATGTGTACTCCCACACTGCACATAGTTATTATCA
1 TCATGTGCACTCCCACACCACACATAGTTATCATCA
1335575 TCATG
1 TCATG
1335580 AGCTCCCATA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.30
Consensus pattern (36 bp):
TCATGTGCACTCCCACACCACACATAGTTATCATCA
Found at i:1344456 original size:25 final size:22
Alignment explanation
Indices: 1344411--1344452 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1344401 TATAGTTTAT
1344411 TTTGATATTTTATTATACAAAA
1 TTTGATATTTTATTATACAAAA
*
1344433 TTTGATTTTTTATTATACAA
1 TTTGATATTTTATTATACAA
1344453 CAAACAATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (22 bp):
TTTGATATTTTATTATACAAAA
Found at i:1344807 original size:21 final size:22
Alignment explanation
Indices: 1344777--1344840 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 22
1344767 TTTGTCATGA
1344777 TTTT-AAATAAAT-TTATTAAT
1 TTTTAAAATAAATATTATTAAT
1344797 TTTTAAAATAAATATT-TT-AT
1 TTTTAAAATAAATATTATTAAT
*
1344817 TTTAAAAATATAAATATTATTAAT
1 TTT-TAAA-ATAAATATTATTAAT
1344841 AAAAATAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
20 9 0.24
21 13 0.35
22 11 0.30
23 2 0.05
24 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTAAAATAAATATTATTAAT
Found at i:1344812 original size:19 final size:21
Alignment explanation
Indices: 1344777--1344826 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
1344767 TTTGTCATGA
1344777 TTTT-AAATAAATT-TATTAAT
1 TTTTAAAATAAATTAT-TTAAT
*
1344797 TTTTAAAATAAA-TATTTTAT
1 TTTTAAAATAAATTATTTAAT
*
1344817 TTTAAAAATA
1 TTTTAAAATA
1344827 TAAATATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTAAAATAAATTATTTAAT
Found at i:1344859 original size:21 final size:21
Alignment explanation
Indices: 1344819--1344859 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1344809 TATTTTATTT
*
1344819 TAAAAATATAAATATTATTAA
1 TAAAAATATAAATATAATTAA
1344840 TAAAAATAATAAA-ATAATTA
1 TAAAAAT-ATAAATATAATTA
1344860 CTTTTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAAAATATAAATATAATTAA
Found at i:1346459 original size:20 final size:22
Alignment explanation
Indices: 1346414--1346458 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1346404 TATTTAACCA
*
1346414 TTTATATTTTATGTATTATAGT
1 TTTATATTTTATATATTATAGT
1346436 TTTATA-TTTAGTATATTA-AGT
1 TTTATATTTTA-TATATTATAGT
1346457 TT
1 TT
1346459 AAATTGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (22 bp):
TTTATATTTTATATATTATAGT
Found at i:1356531 original size:17 final size:17
Alignment explanation
Indices: 1356509--1356546 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1356499 CTATGTCTAG
1356509 ATAATATATT-TATATTA
1 ATAATA-ATTGTATATTA
*
1356526 ATAATAATTGTATTTTA
1 ATAATAATTGTATATTA
1356543 ATAA
1 ATAA
1356547 CTTTAGCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
ATAATAATTGTATATTA
Found at i:1385141 original size:28 final size:29
Alignment explanation
Indices: 1385080--1385141 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 29
1385070 CTTATAATTT
* * *
1385080 TAATTTTTTTATATTATATTTTATGGGTA
1 TAATTTTTTTATATTACATCTTATGGATA
1385109 T--TTTTTTTA-ATTACATCTTATGGATA
1 TAATTTTTTTATATTACATCTTATGGATA
1385135 TAATTTT
1 TAATTTT
1385142 ATTTTCACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 15 0.54
27 8 0.29
28 4 0.14
29 1 0.04
ACGTcount: A:0.27, C:0.03, G:0.08, T:0.61
Consensus pattern (29 bp):
TAATTTTTTTATATTACATCTTATGGATA
Found at i:1395282 original size:19 final size:19
Alignment explanation
Indices: 1395258--1395294 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1395248 GAACAGGTTT
1395258 TCTTTTGTTTTACATTCTG
1 TCTTTTGTTTTACATTCTG
* *
1395277 TCTTTTTTTTTACTTTCT
1 TCTTTTGTTTTACATTCT
1395295 CTGGTTGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.08, C:0.16, G:0.05, T:0.70
Consensus pattern (19 bp):
TCTTTTGTTTTACATTCTG
Found at i:1398406 original size:2 final size:2
Alignment explanation
Indices: 1398399--1398429 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1398389 CCCTTTTTCA
1398399 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1398430 AATTCAGTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1418418 original size:27 final size:27
Alignment explanation
Indices: 1418300--1418440 Score: 84
Period size: 27 Copynumber: 5.2 Consensus size: 27
1418290 CATTATGATG
* *
1418300 TATAACAATTAAAATTTTCAACATGACA
1 TATAACAATT-AAATTTTTAACATAACA
* * * ** * *
1418328 TTTAATAACTAAACCTTCATCATAACA
1 TATAACAATTAAATTTTTAACATAACA
* ** * **
1418355 TATAACAATTAATTTTTTATTATGATG
1 TATAACAATTAAATTTTTAACATAACA
* * *
1418382 TGTAATAATTAAATTTTTAACATAACG
1 TATAACAATTAAATTTTTAACATAACA
* * *
1418409 TATAACAATTAAATCTTCAACATGACA
1 TATAACAATTAAATTTTTAACATAACA
1418436 TATAA
1 TATAA
1418441 TTATATTTTT
Statistics
Matches: 82, Mismatches: 31, Indels: 1
0.72 0.27 0.01
Matches are distributed among these distances:
27 75 0.91
28 7 0.09
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.38
Consensus pattern (27 bp):
TATAACAATTAAATTTTTAACATAACA
Found at i:1418437 original size:81 final size:79
Alignment explanation
Indices: 1418285--1418485 Score: 208
Period size: 81 Copynumber: 2.5 Consensus size: 79
1418275 ATCTAACAAC
* * * * * * *
1418285 TTTTTCATTATGATGTATAACAATTAAAATTTTCAACATGACATTTAATAACTAAACCTTCATCA
1 TTTTTTATTATGATGTGTAATAATT-AAATTTTCAACATAACATATAACAACTAAACCTTCAACA
1418350 TAACATATAACAATTA-A
65 TAACATAT---AATTATA
* * * *
1418367 TTTTTTATTATGATGTGTAATAATTAAATTTTTAACATAACGTATAACAATTAAATCTTCAACAT
1 TTTTTTATTATGATGTGTAATAATTAAATTTTCAACATAACATATAACAACTAAACCTTCAACAT
*
1418432 GACATATAATTATA
66 AACATATAATTATA
* * *
1418446 TTTTTTAATT-TAACGTGTAATAATTATATTTTCAACATAA
1 TTTTTT-ATTATGATGTGTAATAATTAAATTTTCAACATAA
1418486 TTTTTTGTCA
Statistics
Matches: 101, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
78 5 0.05
79 33 0.33
80 3 0.03
81 38 0.38
82 22 0.22
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (79 bp):
TTTTTTATTATGATGTGTAATAATTAAATTTTCAACATAACATATAACAACTAAACCTTCAACAT
AACATATAATTATA
Found at i:1418461 original size:52 final size:51
Alignment explanation
Indices: 1418386--1418483 Score: 124
Period size: 52 Copynumber: 1.9 Consensus size: 51
1418376 ATGATGTGTA
1418386 ATAATTAAATTTTTAACATAACGTATAACAATTAAATCTTCAACATGACAT
1 ATAATTAAATTTTTAACATAACGTATAACAATTAAATCTTCAACATGACAT
* ** * * * *
1418437 ATAATTATATTTTTTAATTTAACGTGTAATAATTATATTTTCAACAT
1 ATAATTA-AATTTTTAACATAACGTATAACAATTAAATCTTCAACAT
1418484 AATTTTTTGT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
51 7 0.18
52 32 0.82
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (51 bp):
ATAATTAAATTTTTAACATAACGTATAACAATTAAATCTTCAACATGACAT
Found at i:1418606 original size:22 final size:22
Alignment explanation
Indices: 1418565--1418604 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1418555 TATTTAATTT
1418565 TTTAATTATTATAATTAAAATA
1 TTTAATTATTATAATTAAAATA
1418587 TTTAATT-TT-TAATTAAAA
1 TTTAATTATTATAATTAAAA
1418605 AAACTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTAATTATTATAATTAAAATA
Found at i:1418615 original size:30 final size:30
Alignment explanation
Indices: 1418534--1418618 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 30
1418524 AACTTAACCC
1418534 TTAATTATAAAAAATAAAAAATATTTAATTTT
1 TTAATTA-AAAAAAT-AAAAATATTTAATTTT
** * *
1418566 TTAATTATTATAATTAAAATATTTAA-TTT
1 TTAATTAAAAAAATAAAAATATTTAATTTT
*
1418595 TTAATTAAAAAAACTCAAAATATT
1 TTAATTAAAAAAA-TAAAAATATT
1418619 AATCTTAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
29 13 0.30
30 20 0.45
31 4 0.09
32 7 0.16
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (30 bp):
TTAATTAAAAAAATAAAAATATTTAATTTT
Found at i:1419553 original size:25 final size:27
Alignment explanation
Indices: 1419510--1419562 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
1419500 TCTAATAATT
* *
1419510 AATGATTAATTAATTATTATTAATTAA
1 AATGATTAATTAATCATTACTAATTAA
*
1419537 AATG-TTAATT-ATCATTACTAGTTAA
1 AATGATTAATTAATCATTACTAATTAA
1419562 A
1 A
1419563 GGATAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 13 0.57
26 6 0.26
27 4 0.17
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (27 bp):
AATGATTAATTAATCATTACTAATTAA
Found at i:1423633 original size:10 final size:10
Alignment explanation
Indices: 1423615--1423654 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
1423605 TATTTTTTTC
1423615 ATAAAAAATA
1 ATAAAAAATA
*
1423625 ATAATAAATA
1 ATAAAAAATA
*
1423635 ATAACAAATA
1 ATAAAAAATA
*
1423645 ACAAAAAATA
1 ATAAAAAATA
1423655 TCAATCAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (10 bp):
ATAAAAAATA
Found at i:1440737 original size:30 final size:32
Alignment explanation
Indices: 1440678--1440737 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 32
1440668 TTTTAAAAAA
* *
1440678 TTAATAAAAATTATATAATAATTTTTTTAAAT
1 TTAATAAAAATTATAAAATAATCTTTTTAAAT
*
1440710 TTAAT-AAAA-TATAAAATTATCTTTTTAA
1 TTAATAAAAATTATAAAATAATCTTTTTAA
1440738 TATTATCATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 16 0.64
31 4 0.16
32 5 0.20
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (32 bp):
TTAATAAAAATTATAAAATAATCTTTTTAAAT
Found at i:1442134 original size:2 final size:2
Alignment explanation
Indices: 1442129--1442153 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1442119 CTCTTAACCC
1442129 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
1442154 CACCCCCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1459480 original size:27 final size:28
Alignment explanation
Indices: 1459450--1459506 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
1459440 AATTAACCGT
*
1459450 TAAAAGAATAATAACAT-TA-TTTTAAAA
1 TAAAAGAA-AATAAAATATATTTTTAAAA
*
1459477 TAAAAGAAATTAAAATATATTTTTAAAA
1 TAAAAGAAAATAAAATATATTTTTAAAA
1459505 TA
1 TA
1459507 TTTTGAGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 6 0.23
27 10 0.38
28 10 0.38
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (28 bp):
TAAAAGAAAATAAAATATATTTTTAAAA
Found at i:1464100 original size:2 final size:2
Alignment explanation
Indices: 1464095--1464137 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
1464085 TCTCTAGGAG
* * * *
1464095 GT GT GT GT CT CT GT GT CT CT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1464137 G
1 G
1464138 CGCTTTTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.09, G:0.42, T:0.49
Consensus pattern (2 bp):
GT
Found at i:1469253 original size:261 final size:260
Alignment explanation
Indices: 1468544--1469478 Score: 916
Period size: 261 Copynumber: 3.6 Consensus size: 260
1468534 CCCTCTCACA
** * * *
1468544 TTTGTTCTTTGATATTTGCCCTTTGGAGCTCTTTGAAGTC-TAT--ATATATATAAATACATGAT
1 TTTGTTCTTCAATATTTGCCCTTTGAAGCTCTTTGAAGCCATATACATATATATAAACACATGAT
* * ** * * * * * *
1468606 ATAGCACTTGTTTAGAAAGTTGCAGCGGAAAAA-CCAAAGC-AAGTTATTACATTGATAGGATGC
66 ACAACACTCATTTAGAAAGCTACAAC-AAAAAAGCCAAAGCTAAGTTATTACATCGATAGCATGC
** * * * *
1468669 TCACCTCAGACCGCTTT-GCATGTTGGCATCGATCATTCTCAGTATCAGTACTAAGAGCCAATGT
130 TCACCTCAGATTGCTTTCG-ATGTTGACATCGATCATTCTCAGCATCAGTATTAA-AGCTAATGT
* ** * *
1468733 TATTTTCTTTGGAAAGTTTGCTTGGTCAAACTTAGAACCCAAAGCTACTTGCTTCCTCTTTCTCC
193 TATTTTCTTTAGAGGGTTTGCTTGGTCAAACTTAGAACCTAAAGCT-CTTGCTTCCTTTTTCTCC
1468798 CATG
257 CATG
* * * * * * * *
1468802 TATGTTCTTGAATATTTGCCTTTTGGAGTTCTTTGAAGCCTACACAAACACACATAGATATAAAC
1 TTTGTTCTTCAATATTTGCCCTTTGAAGCTCTTTGAAG----C-C--ATATACATATATATAAAC
* * * * *
1468867 ACATGATGCAATAGTCATTCAGAAAGCTACAATAAAAAAGCCAAAGCTAAGTTATTACATCGATA
59 ACATGATACAACACTCATTTAGAAAGCTACAACAAAAAAGCCAAAGCTAAGTTATTACATCGATA
* * * * *
1468932 TCATGTTCACCTCAGATTGCTTCCCATGTTGACATCGATCATTCTCAGCATTAGTATTAAACGCT
124 GCATGCTCACCTCAGATTGCTTTCGATGTTGACATCGATCATTCTCAGCATCAGTATTAAA-GCT
** * * *
1468997 AATGTTATTTTCTCCATAGGGATTGCTTGGTCAAAC-TCGTAACCTAAAGCTGCTTGCTTCCTTT
188 AATGTTATTTTCTTTAGAGGGTTTGCTTGGTCAAACTTAG-AACCTAAAGCT-CTTGCTTCCTTT
1469061 TTCTCCCATG
251 TTCTCCCATG
* * * *
1469071 TTTGTTCTTCAATATTTGTCCTTTGAAGCTTTTTGAAG-CATATATATATATATAAACACGTGAT
1 TTTGTTCTTCAATATTTGCCCTTTGAAGCTCTTTGAAGCCATATACATATATATAAACACATGAT
* *
1469135 ACAACACTCATTTAGAAAGGTGCAACAAAAAAGCCAAAGCTAAGTTATTACATCGATAGCATGCT
66 ACAACACTCATTTAGAAAGCTACAACAAAAAAGCCAAAGCTAAGTTATTACATCGATAGCATGCT
* * * * **
1469200 CACTTCAGATTGCTTTCGATGTTGACATCGATTATTCTTAGCATCAATATTAAAAATCAATGTTA
131 CACCTCAGATTGCTTTCGATGTTGACATCGATCATTCTCAGCATCAGTATTAAAGCT-AATGTTA
* *
1469265 TTTTCTTTAGAGGGTTTGCTTGGTTAAACTTAGAACCTGAAGCTCTTTGCTTCCTTTTTCTCCCA
195 TTTTCTTTAGAGGGTTTGCTTGGTCAAACTTAGAACCTAAAGCTC-TTGCTTCCTTTTTCTCCCA
*
1469330 CG
259 TG
* * * *
1469332 GTTGTTCTTCGATATTTGCCCTTTGAAGCACTTT-AAGTCTACATATACATATATATAAACATAT
1 TTTGTTCTTCAATATTTGCCCTTTGAAGCTCTTTGAAG-C--CATATACATATATATAAACACAT
* ** * * * * *
1469396 GATGCAGTACTCATTTAGAAAGCTACAGCAAAGAAGCCAAAGTTAAAGTTATCAAATCGATAGCA
63 GATACAACACTCATTTAGAAAGCTACAACAAAAAAGCCAAAGCT-AAGTTATTACATCGATAGCA
* * *
1469461 TGATCTCCTTAGATTGCT
127 TGCTCACCTCAGATTGCT
1469479 CTCCGTTTAA
Statistics
Matches: 547, Mismatches: 107, Indels: 39
0.79 0.15 0.06
Matches are distributed among these distances:
258 33 0.06
260 5 0.01
261 213 0.39
262 2 0.00
263 2 0.00
264 56 0.10
265 32 0.06
266 1 0.00
267 5 0.01
268 41 0.07
269 157 0.29
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.35
Consensus pattern (260 bp):
TTTGTTCTTCAATATTTGCCCTTTGAAGCTCTTTGAAGCCATATACATATATATAAACACATGAT
ACAACACTCATTTAGAAAGCTACAACAAAAAAGCCAAAGCTAAGTTATTACATCGATAGCATGCT
CACCTCAGATTGCTTTCGATGTTGACATCGATCATTCTCAGCATCAGTATTAAAGCTAATGTTAT
TTTCTTTAGAGGGTTTGCTTGGTCAAACTTAGAACCTAAAGCTCTTGCTTCCTTTTTCTCCCATG
Found at i:1469724 original size:266 final size:267
Alignment explanation
Indices: 1469311--1469809 Score: 671
Period size: 267 Copynumber: 1.9 Consensus size: 267
1469301 CTGAAGCTCT
* *
1469311 TTGCTTCCTTTTTCTCCCACGGTTGTTCTTCGATATTTGCCCTTTGAAGCACTTTAAGTCTACAT
1 TTGCTTCCCTTTTCTCCCACGGTTGTTCTTCAATATTTGCCCTTTGAAGCACTTTAAGTCTACAT
* * * * * **
1469376 ATACATATATATAAACATATGATGCAGTACTCATTTAGAAAGCTACAGCAAAGAAGCCAAAGTTA
66 ATACA-ATATATAAACACATGATGCAATACTCATTCAGAAAGCTACAACAAAAAAGCCAAAACTA
* * * * *
1469441 AAGTTATCAAATCGATAGCATGATCTCCTTAGATTGCTCTCCGT-TTAATGTACTGCCATAGATG
130 AAGTTATCAAATCGATAGCATGATCACCTAAGACTGATCTCCATGTTAATGTACTGCCATAGATG
*
1469505 TATGCTCATTTTGTTACCTTGTGGCTTGCTTATCATTTAAGTTTACATAATCAAACTTAAAACGT
195 TATGCTCATGTTGTTACCTTGTGGCTTGCTTATCATTTAAGTTTACATAATCAAACTTAAAACGT
1469570 GAAGTTGC
260 GAAGTTGC
* * * * *
1469578 TTGCTTCCCTTTTCTCCCATGTTTGTTCTTCAATATTTGCCTTTTGGAGCTCTTTAAAG-CTTAC
1 TTGCTTCCCTTTTCTCCCACGGTTGTTCTTCAATATTTGCCCTTTGAAGCACTTT-AAGTC-TAC
* * * *
1469642 ATATAC-ATCTATAAACACATGGTGCAATATTCATTCAGAAAGCTCCAACAAAAAAGCCAAAACT
64 ATATACAATATATAAACACATGATGCAATACTCATTCAGAAAGCTACAACAAAAAAGCCAAAACT
* * * * * *
1469706 AAAGTTATCACATCGATAGCATGCTCACCTAATACTGATCTCCATGTTGATGTAGTGTCATAGAT
129 AAAGTTATCAAATCGATAGCATGATCACCTAAGACTGATCTCCATGTTAATGTACTGCCATAGAT
*
1469771 GTATGCTCATGTTGTTGCCTTGTGGCTTGCTTATCATTT
194 GTATGCTCATGTTGTTACCTTGTGGCTTGCTTATCATTT
1469810 TCTTGTCTTG
Statistics
Matches: 198, Mismatches: 31, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
266 84 0.42
267 102 0.52
268 12 0.06
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.36
Consensus pattern (267 bp):
TTGCTTCCCTTTTCTCCCACGGTTGTTCTTCAATATTTGCCCTTTGAAGCACTTTAAGTCTACAT
ATACAATATATAAACACATGATGCAATACTCATTCAGAAAGCTACAACAAAAAAGCCAAAACTAA
AGTTATCAAATCGATAGCATGATCACCTAAGACTGATCTCCATGTTAATGTACTGCCATAGATGT
ATGCTCATGTTGTTACCTTGTGGCTTGCTTATCATTTAAGTTTACATAATCAAACTTAAAACGTG
AAGTTGC
Done.